Nanoparticles are known to play remarkable role as abiotic stress elicitors in plants. This study reports the comparative analysis of effects produced by capped [zinc oxide (ZnO)-polyethylene glycol (PEG), ZnO-polyvinyl pyrrolidone (PVP), copper oxide (CuO)-PEG, CuO-PVP] and uncapped (ZnO and CuO) nanoparticles on the medicinal plant, Stevia rebaudiana raised in vitro for the production of commercially important sweetener compounds. In context of shoot organogenesis, ZnO-PEG, ZnO-PVP, CuO-PEG, CuO-PVP were employed to the growth medium that resulted in increased growth parameters, and larger content of steviol glycosides as compared to the shoots raised in medium containing ZnO and CuO, revealed by high-performance liquid chromatography. In the meanwhile, non-enzymatic antioxidant activities including total phenolic content, total flavonoid content, total antioxidant capacity, total reducing power and 2,2-diphenyl-1-picryl hydrazyl-free radical scavenging activity were calculated and showed comparatively greater amounts in shoots grown in medium containing capped ZnO or CuO nanoparticles. Furthermore, the ZnO and its derivatives revealed to be more reactive at 1 mg/l of concentration. Whereas, the CuO and its derivatives produced greater response on Stevia at 10 mg/l concentration of nanoparticles. This study paves the way for more such studies encompassing capped and uncapped nanoparticles and their ultimate effect on in-vitro grown plant tissues for the production of active metabolites on industrial scale.